I had troubles finding a way to transcode audio files. I needed something with a graphical user interface (GUI), that would automatically name the output files, handle multiple files at a time, give me a fairly wide choice of types of file output (flac, mp3, wav, etc) and would "just work" as my tech skills are not the greatest.

Then I installed Clementine and everything went smoothly after that.

This tutorial is for others with a low skill level. I am using Linux Mint Mate 18.3 on an older machine and Clementine version 1.2.3

Recipe
Part AInstall Clementine.
From Menu go to Software Manager.
In the search box up the top right of Software Manager type in Clementine.
Click in the box that says Clementine modern music player and library organiser
Click on Install
If a pop-up box appears that reads in part, 'Additional software has to be installed' then click Continue
Then provide your password.
Wait while the program is installed.
once Clementine is installed then close the Software Manager window.

Part BUse Clementine to transcode your audio files.
I suggest making a trial run with only two files to begin with. This will allow you to be relaxed and learn more easily.
Open Clementine by going to Menu then Sound & Video under Applications and then clicking on Clementine.
In the 'Clementine' window click on Tools and then click on Transcode Music
Then click on the Add... button and then, in the 'Add files to transcode' window, navigate to the the audio files you want to make transcoded versions of. Select the desired files and then click 'Open' in the bottom left hand corner of that window.
Or click on the Import ... button to add the directories that contain the files you want to transcode. Then, in the 'Open a directory to import music from', navigate to the directories that contain the files you want to have transcoded, select the desired directories and then click on 'Open' in the bottom left hand corner of that window.
Back in the 'Transcode Music' window, in the box to the right of "Audio format", use the drop down arrow and select the type of audio file that you want for the output.
If you want to make fine adjustments to the audio file output then click on Options... and make the adjustments.
This tutorial will not go into the range of possible adjustments or benefits or costs of particular file types. If you are using the output audio files for important purposes then I suggest you research further to find settings that suit your needs. For a smaller number of general purpose audio files the standard settings will very likely be good enough.
Next decide where you want the newly created audio files to be put by Clementine.
If you want them in a different folder to the original files then click on Select to the right from "Destination" and select or create the folder that the new files will be placed in by Clementine.
Look in the box to the right of "Destination" to check that your choice is correctly displayed. I have had a couple of times where I have had to go back and Select the desired Destination directory again.
Click Start transcoding
Wait while the files are transcoded.
The progress bar will show you how much has been done. Large files or many files can take some time to transcode.
If you want to, navigate to your chosen output directory and listen to one of your newly transcoded audio files.

Personally I use "soundkonverter" for converting audio files. It will do pretty much everything you said you want to do with your audio files. It is in the repositories and you can give it shot if you want.

Please notice that it is spelled with "k" for not to be mistaken with another one named simply "soundconverter". Of the latter I have no experience.

In the Grand Scheme of Things, everything on Earth is nothing but an annoying Bug.

It is a stand-alone program just built for transcoding.
After installing it and trying to run it it wouldn't work but gave me instructions. The instructions were just a bit above my skill level so I guessed and opened a terminal and cut kbuildsycoca4 from the pop-up message and then pasted

kbuildsycoca4

into the terminal and typed Enter.
I then closed and then re-opened soundKonverter and it worked fine.

It gives more audio file types as output options than Clementine.

If a person had even low-medium skill levels, soundKonverter, as probably the more powerful program for transcoding audio file, would be my first suggestion.
As a low skill level person I found Clementine easier to install.

I've just tried both Clementine and soundKonverter, looking to convert / transcode a file from youtube with a .webm extension.
Neither seem able to handle webm files.
This just being a single file I suppose this is a good time to learn how to use FFmpeg in a terminal.

Though my other option would be to download the whole thing again and tell youtube-dl to use ffmpeg to transcode / convert the audio automagically to mp3 or ogg.